forester/java/src/org/forester/application/gsdi.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.FilenameFilter;
  30 import java.io.IOException;
  31 import java.text.SimpleDateFormat;
  32 import java.util.ArrayList;
  33 import java.util.Arrays;
  34 import java.util.Date;
  35 import java.util.List;
  36 import java.util.SortedMap;
  37 import java.util.SortedSet;
  38 import java.util.TreeMap;
  39 import java.util.TreeSet;
  40
  41 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  42 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  43 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  44 import org.forester.io.writers.PhylogenyWriter;
  45 import org.forester.phylogeny.Phylogeny;
  46 import org.forester.phylogeny.PhylogenyMethods;
  47 import org.forester.phylogeny.PhylogenyNode;
  48 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  49 import org.forester.phylogeny.factories.PhylogenyFactory;
  50 import org.forester.sdi.GSDI;
  51 import org.forester.sdi.GSDII;
  52 import org.forester.sdi.GSDIR;
  53 import org.forester.sdi.SDIException;
  54 import org.forester.sdi.SDIutil;
  55 import org.forester.sdi.SDIutil.ALGORITHM;
  56 import org.forester.util.CommandLineArguments;
  57 import org.forester.util.EasyWriter;
  58 import org.forester.util.ForesterConstants;
  59 import org.forester.util.ForesterUtil;
  60
  61 public final class gsdi {
  62
  63     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
  64     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION    = "g";
  65     final static private String GSDIR_OPTION                           = "r";
  66     final static private String MOST_PARSIMONIOUS_OPTION               = "m";
  67     final static private String SUFFIX_FOR_DIR_OPTION                  = "s";
  68     final static private String GUESS_FORMAT_OF_SPECIES_TREE           = "q";
  69     final static private String TRANSFER_TAXONOMY_OPTION               = "t";
  70     final static private String HELP_OPTION_1                          = "help";
  71     final static private String HELP_OPTION_2                          = "h";
  72     final static private String SUFFIX_FOR_SPECIES_TREE_USED           = "_species_tree_used.xml";
  73     final static private String OUTTREE_SUFFIX                         = "_gsdir.xml";
  74     final static private String LOGFILE_NAME                           = "00_gsdi_log.tsv";
  75     final static private String LOGFILE_SUFFIX                         = "_gsdi_log.txt";
  76     final static private String REMAPPED_SUFFIX                        = "_gsdi_remapped.txt";
  77     final static private String PRG_NAME                               = "gsdi";
  78     final static private String PRG_VERSION                            = "1.100";
  79     final static private String PRG_DATE                               = "170403";
  80     final static private String PRG_DESC                               = "general speciation duplication inference";
  81     final static private String E_MAIL                                 = "phyloxml@gmail.com";
  82     final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/forester";
  83
  84     public static void main( final String args[] ) {
  85         try {
  86             ForesterUtil.printProgramInformation( PRG_NAME,
  87                                                   PRG_DESC,
  88                                                   PRG_VERSION,
  89                                                   PRG_DATE,
  90                                                   E_MAIL,
  91                                                   WWW,
  92                                                   ForesterUtil.getForesterLibraryInformation() );
  93             CommandLineArguments cla = null;
  94             try {
  95                 cla = new CommandLineArguments( args );
  96             }
  97             catch ( final Exception e ) {
  98                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  99             }
 100             if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
 101                 System.out.println();
 102                 gsdi.print_help();
 103                 System.exit( 0 );
 104             }
 105             else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) {
 106                 System.out.println();
 107                 System.out.println( "Wrong number of arguments." );
 108                 System.out.println();
 109                 gsdi.print_help();
 110                 System.exit( -1 );
 111             }
 112             final List<String> allowed_options = new ArrayList<String>();
 113             allowed_options.add( GSDIR_OPTION );
 114             allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE );
 115             allowed_options.add( MOST_PARSIMONIOUS_OPTION );
 116             allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 117             allowed_options.add( TRANSFER_TAXONOMY_OPTION );
 118             allowed_options.add( SUFFIX_FOR_DIR_OPTION );
 119             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 120             if ( dissallowed_options.length() > 0 ) {
 121                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
 122             }
 123             execute( cla );
 124         }
 125         catch ( final IOException e ) {
 126             ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
 127         }
 128     }
 129
 130     private final static void execute( final CommandLineArguments cla ) throws IOException {
 131         ALGORITHM base_algorithm = ALGORITHM.GSDI;
 132         boolean most_parsimonous_duplication_model = false;
 133         boolean allow_stripping_of_gene_tree = false;
 134         if ( cla.isOptionSet( GSDIR_OPTION ) ) {
 135             base_algorithm = ALGORITHM.GSDIR;
 136         }
 137         if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
 138             if ( base_algorithm == ALGORITHM.SDI ) {
 139                 ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
 140             }
 141             most_parsimonous_duplication_model = true;
 142         }
 143         if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 144             if ( base_algorithm == ALGORITHM.SDI ) {
 145                 ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
 146             }
 147             allow_stripping_of_gene_tree = true;
 148         }
 149         boolean transfer_taxonomy = false;
 150         if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) {
 151             transfer_taxonomy = true;
 152         }
 153         boolean use_gene_tree_dir = false;
 154         final String gene_tree_suffix;
 155         if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) {
 156             gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION );
 157             use_gene_tree_dir = true;
 158         }
 159         else {
 160             gene_tree_suffix = null;
 161         }
 162         File gene_tree_file = null;
 163         File species_tree_file = null;
 164         File out_file = null;
 165         File log_file = null;
 166         File out_dir = null;
 167         try {
 168             gene_tree_file = cla.getFile( 0 );
 169             species_tree_file = cla.getFile( 1 );
 170             if ( use_gene_tree_dir ) {
 171                 out_dir = cla.getFile( 2 );
 172                 if ( out_dir.exists() ) {
 173                     if ( !out_dir.isDirectory() ) {
 174                         ForesterUtil
 175                                 .fatalError( gsdi.PRG_NAME,
 176                                              "out-directory [" + out_dir + "] already exists but is not a directory" );
 177                     }
 178                 }
 179                 else {
 180                     final boolean success = out_dir.mkdirs();
 181                     if ( !success ) {
 182                         ForesterUtil.fatalError( gsdi.PRG_NAME, "could not create out-directory [" + out_dir + "]" );
 183                     }
 184                 }
 185             }
 186             else {
 187                 out_file = cla.getFile( 2 );
 188                 log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 189             }
 190         }
 191         catch ( final IllegalArgumentException e ) {
 192             ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
 193         }
 194         if ( use_gene_tree_dir ) {
 195             final File indir = new File( gene_tree_file.toString() );
 196             if ( !indir.exists() ) {
 197                 ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] does not exist" );
 198             }
 199             if ( !indir.isDirectory() ) {
 200                 ForesterUtil.fatalError( gsdi.PRG_NAME, "in-directory [" + indir + "] is not a directory" );
 201             }
 202             final String species_tree_file_name = species_tree_file.getName();
 203             final File gene_tree_files[] = indir.listFiles( new FilenameFilter() {
 204
 205                 @Override
 206                 public boolean accept( final File dir, final String name ) {
 207                     return ( ( name.endsWith( gene_tree_suffix ) ) && !( name.equals( species_tree_file_name ) ) );
 208                 }
 209             } );
 210             if ( gene_tree_files.length < 1 ) {
 211                 ForesterUtil.fatalError( gsdi.PRG_NAME,
 212                                          "in-directory [" + indir
 213                                                  + "] does not contain any gene tree files with suffix "
 214                                                  + gene_tree_suffix );
 215             }
 216             executeDir( base_algorithm,
 217                         most_parsimonous_duplication_model,
 218                         allow_stripping_of_gene_tree,
 219                         transfer_taxonomy,
 220                         gene_tree_files,
 221                         species_tree_file,
 222                         out_dir );
 223         }
 224         else {
 225             execute( base_algorithm,
 226                      most_parsimonous_duplication_model,
 227                      allow_stripping_of_gene_tree,
 228                      transfer_taxonomy,
 229                      gene_tree_file,
 230                      species_tree_file,
 231                      out_file,
 232                      log_file );
 233         }
 234     }
 235
 236     private final static void executeDir( final ALGORITHM base_algorithm,
 237                                           final boolean most_parsimonous_duplication_model,
 238                                           final boolean allow_stripping_of_gene_tree,
 239                                           final boolean transfer_taxonomy,
 240                                           final File gene_tree_files[],
 241                                           final File species_tree_file,
 242                                           final File outdir )
 243             throws IOException {
 244         final File log_file = new File( outdir, LOGFILE_NAME );
 245         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 246             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 247         }
 248         EasyWriter log_writer = null;
 249         try {
 250             log_writer = ForesterUtil.createEasyWriter( log_file );
 251         }
 252         catch ( final IOException e ) {
 253             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 254         }
 255         log_writer.println( "# " + PRG_NAME );
 256         log_writer.println( "# Version\t" + PRG_VERSION );
 257         log_writer.println( "# Date\t" + PRG_DATE );
 258         log_writer.println( "# Forester version\t" + ForesterConstants.FORESTER_VERSION );
 259         log_writer.println( "# Species tree\t" + species_tree_file.getCanonicalPath() );
 260         if ( base_algorithm == ALGORITHM.GSDI ) {
 261             log_writer.println( "# Algorithm\tGSDI" );
 262         }
 263         else if ( base_algorithm == ALGORITHM.GSDIR ) {
 264             log_writer.println( "# Algorithm\tGSDIR" );
 265         }
 266         log_writer.println( "# Use most parsimonous duplication model\t" + most_parsimonous_duplication_model );
 267         log_writer.println( "# Allow stripping of gene tree nodes\t" + allow_stripping_of_gene_tree );
 268         log_writer.println( "# Start time\t" + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 269         log_writer.println();
 270         log_writer.print( "Gene-tree file\t" );
 271         log_writer.print( "Gene-tree name/#\t" );
 272         log_writer.print( "Ext. nodes\t" );
 273         log_writer.print( "Speciations\t" );
 274         log_writer.print( "Duplications\t" );
 275         if ( !most_parsimonous_duplication_model ) {
 276             log_writer.print( "Spec. or Dup.\t" );
 277         }
 278         if ( allow_stripping_of_gene_tree ) {
 279             log_writer.print( "Stripped gene-tree ext. nodes\t" );
 280         }
 281         log_writer.print( "Taxonomy mapping" );
 282         log_writer.println();
 283         int counter = 0;
 284         Arrays.sort( gene_tree_files );
 285         for( final File gene_tree_file : gene_tree_files ) {
 286             String outname = gene_tree_file.getName();
 287             if ( outname.indexOf( "." ) > 0 ) {
 288                 outname = outname.substring( 0, outname.lastIndexOf( "." ) );
 289             }
 290             outname = outname + OUTTREE_SUFFIX;
 291             counter += executeOneTreeInDir( base_algorithm,
 292                                             most_parsimonous_duplication_model,
 293                                             allow_stripping_of_gene_tree,
 294                                             transfer_taxonomy,
 295                                             gene_tree_file,
 296                                             species_tree_file,
 297                                             new File( outdir, outname ),
 298                                             log_writer );
 299             log_writer.flush();
 300             System.out.print( "\r" + counter );
 301         }
 302         System.out.print( "\r" );
 303         log_writer.close();
 304         System.out.println( "Analyzed " + counter + " gene trees" );
 305         System.out.println();
 306         System.out.println( "Wrote log to: " + log_file.getCanonicalPath() );
 307         System.out.println();
 308     }
 309
 310     private final static int executeOneTreeInDir( final ALGORITHM base_algorithm,
 311                                                   final boolean most_parsimonous_duplication_model,
 312                                                   final boolean allow_stripping_of_gene_tree,
 313                                                   final boolean transfer_taxonomy,
 314                                                   final File gene_tree_file,
 315                                                   final File species_tree_file,
 316                                                   final File out_file,
 317                                                   final EasyWriter log_writer )
 318             throws IOException {
 319         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 320             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 321         }
 322         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 323             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 324         }
 325         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 326             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 327         }
 328         Phylogeny gene_trees[] = null;
 329         try {
 330             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 331             gene_trees = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() );
 332         }
 333         catch ( final IOException e ) {
 334             fatalError( "error",
 335                         "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 336                         log_writer );
 337         }
 338         int counter = 0;
 339         final List<Phylogeny> out_trees = new ArrayList<Phylogeny>();
 340         for( final Phylogeny gene_tree : gene_trees ) {
 341             if ( !gene_tree.isEmpty() && gene_tree.getNumberOfExternalNodes() > 1 ) {
 342                 Phylogeny species_tree = null;
 343                 try {
 344                     species_tree = SDIutil.parseSpeciesTree( gene_tree,
 345                                                              species_tree_file,
 346                                                              REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
 347                                                              true,
 348                                                              TAXONOMY_EXTRACTION.NO );
 349                 }
 350                 catch ( final PhyloXmlDataFormatException e ) {
 351                     fatalError( "user error",
 352                                 "failed to transfer general node name, in [" + species_tree_file + "]: "
 353                                         + e.getMessage(),
 354                                 log_writer );
 355                 }
 356                 catch ( final SDIException e ) {
 357                     fatalError( "user error", e.getMessage(), log_writer );
 358                 }
 359                 catch ( final IOException e ) {
 360                     fatalError( "error",
 361                                 "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 362                                 log_writer );
 363                 }
 364                 gene_tree.setRooted( true );
 365                 species_tree.setRooted( true );
 366                 if ( !gene_tree.isCompletelyBinary() ) {
 367                     fatalError( "user error",
 368                                 "gene tree [" + gene_tree_file + "] is not completely binary",
 369                                 log_writer );
 370                 }
 371                 if ( base_algorithm == ALGORITHM.SDI ) {
 372                     if ( !species_tree.isCompletelyBinary() ) {
 373                         fatalError( "user error",
 374                                     "species tree is not completely binary, use GSDI or GSDIR instead",
 375                                     log_writer );
 376                     }
 377                 }
 378                 log_writer.print( gene_tree_file.getName() );
 379                 log_writer.print( "\t" );
 380                 log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 381                 if ( gene_trees.length > 1 ) {
 382                     log_writer.print( ( ForesterUtil.isEmpty( gene_tree.getName() ) ? Integer.toString( counter )
 383                             : ( ":" + Integer.toString( counter ) ) ) );
 384                 }
 385                 log_writer.print( "\t" );
 386                 GSDII gsdii = null;
 387                 try {
 388                     if ( base_algorithm == ALGORITHM.GSDI ) {
 389                         gsdii = new GSDI( gene_tree,
 390                                           species_tree,
 391                                           most_parsimonous_duplication_model,
 392                                           allow_stripping_of_gene_tree,
 393                                           true,
 394                                           transfer_taxonomy );
 395                     }
 396                     else if ( base_algorithm == ALGORITHM.GSDIR ) {
 397                         gsdii = new GSDIR( gene_tree,
 398                                            species_tree,
 399                                            allow_stripping_of_gene_tree,
 400                                            true,
 401                                            transfer_taxonomy );
 402                     }
 403                 }
 404                 catch ( final SDIException e ) {
 405                     fatalError( "user error", e.getLocalizedMessage(), log_writer );
 406                 }
 407                 catch ( final OutOfMemoryError e ) {
 408                     ForesterUtil.outOfMemoryError( e );
 409                 }
 410                 catch ( final Exception e ) {
 411                     e.printStackTrace();
 412                     fatalError( "unexpected error", e.toString(), log_writer );
 413                 }
 414                 if ( base_algorithm == ALGORITHM.GSDIR ) {
 415                     final Phylogeny gt = ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree();
 416                     gt.setRerootable( false );
 417                     out_trees.add( gt );
 418                 }
 419                 else {
 420                     gene_tree.setRerootable( false );
 421                     out_trees.add( gene_tree );
 422                 }
 423                 log_writer.print( gene_tree.getNumberOfExternalNodes() + "\t" );
 424                 log_writer.print( gsdii.getSpeciationsSum() + "\t" );
 425                 if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 426                     final GSDIR gsdir = ( GSDIR ) gsdii;
 427                     log_writer.print( gsdir.getMinDuplicationsSum() + "\t" );
 428                 }
 429                 else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 430                     final GSDI gsdi = ( GSDI ) gsdii;
 431                     log_writer.print( gsdi.getDuplicationsSum() + "\t" );
 432                     if ( !most_parsimonous_duplication_model ) {
 433                         log_writer.print( gsdi.getSpeciationOrDuplicationEventsSum() + "\t" );
 434                     }
 435                 }
 436                 if ( allow_stripping_of_gene_tree ) {
 437                     log_writer.print( gsdii.getStrippedExternalGeneTreeNodes().size() + "\t" );
 438                 }
 439                 log_writer.print( gsdii.getTaxCompBase().toString() );
 440                 log_writer.println();
 441                 ++counter;
 442             }
 443         }
 444         if ( counter > 0 ) {
 445             try {
 446                 final PhylogenyWriter writer = new PhylogenyWriter();
 447                 writer.toPhyloXML( out_file, out_trees, 0, ForesterUtil.LINE_SEPARATOR );
 448             }
 449             catch ( final IOException e ) {
 450                 ForesterUtil
 451                         .fatalError( PRG_NAME,
 452                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 453             }
 454         }
 455         return counter;
 456     }
 457
 458     private final static void execute( final ALGORITHM base_algorithm,
 459                                        final boolean most_parsimonous_duplication_model,
 460                                        final boolean allow_stripping_of_gene_tree,
 461                                        final boolean transfer_taxonomy,
 462                                        final File gene_tree_file,
 463                                        final File species_tree_file,
 464                                        final File out_file,
 465                                        final File log_file )
 466             throws IOException {
 467         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 468             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 469         }
 470         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 471             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 472         }
 473         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 474             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 475         }
 476         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 477             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 478         }
 479         EasyWriter log_writer = null;
 480         try {
 481             log_writer = ForesterUtil.createEasyWriter( log_file );
 482         }
 483         catch ( final IOException e ) {
 484             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 485         }
 486         Phylogeny species_tree = null;
 487         Phylogeny gene_tree = null;
 488         try {
 489             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 490             gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
 491         }
 492         catch ( final IOException e ) {
 493             fatalError( "error",
 494                         "failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 495                         log_writer );
 496         }
 497         try {
 498             species_tree = SDIutil.parseSpeciesTree( gene_tree,
 499                                                      species_tree_file,
 500                                                      REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE,
 501                                                      true,
 502                                                      TAXONOMY_EXTRACTION.NO );
 503         }
 504         catch ( final PhyloXmlDataFormatException e ) {
 505             fatalError( "user error",
 506                         "failed to transfer general node name, in [" + species_tree_file + "]: " + e.getMessage(),
 507                         log_writer );
 508         }
 509         catch ( final SDIException e ) {
 510             fatalError( "user error", e.getMessage(), log_writer );
 511         }
 512         catch ( final IOException e ) {
 513             fatalError( "error",
 514                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 515                         log_writer );
 516         }
 517         gene_tree.setRooted( true );
 518         species_tree.setRooted( true );
 519         if ( !gene_tree.isCompletelyBinary() ) {
 520             fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer );
 521         }
 522         if ( base_algorithm == ALGORITHM.SDI ) {
 523             if ( !species_tree.isCompletelyBinary() ) {
 524                 fatalError( "user error",
 525                             "species tree is not completely binary, use GSDI or GSDIR instead",
 526                             log_writer );
 527             }
 528         }
 529         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 530         log_writer.println( "  version         : " + PRG_VERSION );
 531         log_writer.println( "  date            : " + PRG_DATE );
 532         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 533         log_writer.println();
 534         log_writer.println( "Start time                               : "
 535                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 536         System.out.println( "Start time                               : "
 537                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 538         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 539         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 540         log_writer.println( "Gene tree name                           : "
 541                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 542         System.out.println( "Gene tree name                           : "
 543                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 544         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 545         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 546         log_writer.println( "Species tree name                        : "
 547                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 548         System.out.println( "Species tree name                        : "
 549                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 550         System.out.println( "Transfer taxonomy                        : " + transfer_taxonomy );
 551         GSDII gsdii = null;
 552         final long start_time = new Date().getTime();
 553         try {
 554             if ( base_algorithm == ALGORITHM.GSDI ) {
 555                 System.out.println( "Algorithm                                : GSDI" );
 556                 log_writer.println( "Algorithm                                : GSDI" );
 557             }
 558             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 559                 System.out.println( "Algorithm                                : GSDIR" );
 560                 log_writer.println( "Algorithm                                : GSDIR" );
 561             }
 562             System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 563             System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 564             log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 565             log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 566             log_writer.flush();
 567             if ( base_algorithm == ALGORITHM.GSDI ) {
 568                 gsdii = new GSDI( gene_tree,
 569                                   species_tree,
 570                                   most_parsimonous_duplication_model,
 571                                   allow_stripping_of_gene_tree,
 572                                   true,
 573                                   transfer_taxonomy );
 574             }
 575             else if ( base_algorithm == ALGORITHM.GSDIR ) {
 576                 gsdii = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, true, transfer_taxonomy );
 577             }
 578         }
 579         catch ( final SDIException e ) {
 580             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 581         }
 582         catch ( final IOException e ) {
 583             fatalError( "error", e.toString(), log_writer );
 584         }
 585         catch ( final OutOfMemoryError e ) {
 586             ForesterUtil.outOfMemoryError( e );
 587         }
 588         catch ( final Exception e ) {
 589             e.printStackTrace();
 590             fatalError( "unexpected error", e.toString(), log_writer );
 591         }
 592         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 593                 + "ms" );
 594         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 595                 + "ms" );
 596         System.out.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 597         log_writer.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
 598         try {
 599             final PhylogenyWriter writer = new PhylogenyWriter();
 600             if ( base_algorithm == ALGORITHM.GSDIR ) {
 601                 final Phylogeny gt = ( ( GSDIR ) gsdii ).getMinDuplicationsSumGeneTree();
 602                 gt.setRerootable( false );
 603                 writer.toPhyloXML( out_file, gt, 0 );
 604             }
 605             else {
 606                 gene_tree.setRerootable( false );
 607                 writer.toPhyloXML( out_file, gene_tree, 0 );
 608             }
 609         }
 610         catch ( final IOException e ) {
 611             ForesterUtil.fatalError( PRG_NAME,
 612                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 613         }
 614         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 615         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 616         final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 617                 + SUFFIX_FOR_SPECIES_TREE_USED );
 618         try {
 619             final PhylogenyWriter writer = new PhylogenyWriter();
 620             writer.toPhyloXML( species_tree_used_file, species_tree, 0 );
 621         }
 622         catch ( final IOException e ) {
 623             ForesterUtil.fatalError( PRG_NAME,
 624                                      "Failed to write to [" + species_tree_used_file.getCanonicalPath() + "]: "
 625                                              + e.getMessage() );
 626         }
 627         System.out.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 628         log_writer.println( "Wrote (stripped) species tree to         : " + species_tree_used_file.getCanonicalPath() );
 629         if ( ( gsdii.getReMappedScientificNamesFromGeneTree() != null )
 630                 && !gsdii.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
 631             System.out.println( "Number of gene tree species remapped     : "
 632                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 633             log_writer.println( "Number of gene tree species remapped     : "
 634                     + gsdii.getReMappedScientificNamesFromGeneTree().size() );
 635             writeToRemappedFile( out_file, gsdii.getReMappedScientificNamesFromGeneTree(), log_writer );
 636         }
 637         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 638         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 639         System.out.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 640         log_writer.println( "Number of external nodes in species tree : " + species_tree.getNumberOfExternalNodes() );
 641         final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
 642         System.out.println( "Number of polytomies in species tree     : " + poly );
 643         log_writer.println( "Number of polytomies in species tree     : " + poly );
 644         System.out.println( "External nodes stripped from gene tree   : "
 645                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 646         log_writer.println( "External nodes stripped from gene tree   : "
 647                 + gsdii.getStrippedExternalGeneTreeNodes().size() );
 648         System.out
 649                 .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 650         log_writer
 651                 .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() );
 652         System.out.println();
 653         System.out.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 654         log_writer.println( "Number of speciations                    : " + gsdii.getSpeciationsSum() );
 655         if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
 656             final GSDIR gsdir = ( GSDIR ) gsdii;
 657             System.out.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 658             log_writer.println( "Minimal number of duplications           : " + gsdir.getMinDuplicationsSum() );
 659         }
 660         else if ( ( base_algorithm == ALGORITHM.GSDI ) ) {
 661             final GSDI gsdi = ( GSDI ) gsdii;
 662             System.out.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 663             log_writer.println( "Number of duplications                   : " + gsdi.getDuplicationsSum() );
 664             if ( !most_parsimonous_duplication_model ) {
 665                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 666                 System.out.println( "Number of potential duplications         : " + u );
 667                 log_writer.println( "Number of potential duplications         : " + u );
 668             }
 669         }
 670         log_writer.println();
 671         printMappedNodesToLog( log_writer, gsdii );
 672         log_writer.println();
 673         printStrippedGeneTreeNodesToLog( log_writer, gsdii );
 674         System.out.println();
 675         System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
 676         System.out.println();
 677         log_writer.close();
 678     }
 679
 680     private final static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
 681         try {
 682             log_writer.flush();
 683             log_writer.println();
 684             log_writer.print( type.toUpperCase() + ": " );
 685             log_writer.println( msg );
 686             log_writer.close();
 687         }
 688         catch ( final IOException e ) {
 689             e.printStackTrace();
 690         }
 691         ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
 692     }
 693
 694     private final static void print_help() {
 695         System.out.println( "Usage: " + PRG_NAME
 696                 + " [-options] <gene tree file, or gene trees in-directory> <species tree> <outfile, or out-directory>" );
 697         System.out.println();
 698         System.out.println( "Options:" );
 699         System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 700                 + "         : to allow stripping of gene tree nodes without a matching species" );
 701         System.out.println( " -" + MOST_PARSIMONIOUS_OPTION
 702                 + "         : use most parimonious duplication model for GSDI: " );
 703         System.out.println( "              assign nodes as speciations which would otherwise be assiged" );
 704         System.out.println( "              as potential duplications due to polytomies in the species tree" );
 705         System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE
 706                 + "         : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 707         System.out.println( " -" + GSDIR_OPTION
 708                 + "         : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" );
 709         System.out.println( " -" + TRANSFER_TAXONOMY_OPTION
 710                 + "         : to transfer taxonomic data from species tree to gene tree" );
 711         System.out.println( " -" + SUFFIX_FOR_DIR_OPTION
 712                 + "=<suffix>: suffix for gene trees for analyzing entire directory of trees" );
 713         System.out.println();
 714         System.out.println();
 715         System.out.println( "Gene tree(s):" );
 716         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 717         System.out.println();
 718         System.out.println( "Species tree:" );
 719         System.out.println( " in phyloXML format (unless option -" + GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 720         System.out.println();
 721         System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 722                 + " gene_tree.xml tree_of_life.xml out.xml" );
 723         System.out.println( "          gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " -" + SUFFIX_FOR_DIR_OPTION
 724                 + "=.xml" + " gene_tree_dir tree_of_life.xml out_dir" );
 725         System.out.println( "          gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + " -" + MOST_PARSIMONIOUS_OPTION
 726                 + " -" + GSDIR_OPTION + " -" + TRANSFER_TAXONOMY_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml"
 727                 + " gene_tree_dir tree_of_life.xml out_dir" );
 728         System.out.println();
 729     }
 730
 731     private final static void printMappedNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
 732             throws IOException {
 733         final SortedSet<String> ss = new TreeSet<String>();
 734         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 735             ss.add( n.toString() );
 736         }
 737         log_writer.println( "The following " + ss.size() + " species were used: " );
 738         for( final String s : ss ) {
 739             log_writer.println( "  " + s );
 740         }
 741     }
 742
 743     private final static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDII gsdi )
 744             throws IOException {
 745         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 746         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 747             final String s = n.toString();
 748             if ( sm.containsKey( s ) ) {
 749                 sm.put( s, sm.get( s ) + 1 );
 750             }
 751             else {
 752                 sm.put( s, 1 );
 753             }
 754         }
 755         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 756         for( final String s : sm.keySet() ) {
 757             final int count = sm.get( s );
 758             if ( count == 1 ) {
 759                 log_writer.println( "  " + s );
 760             }
 761             else {
 762                 log_writer.println( "  " + s + " [" + count + "]" );
 763             }
 764         }
 765     }
 766
 767     private final static void writeToRemappedFile( final File out_file,
 768                                                    final SortedSet<String> remapped,
 769                                                    final EasyWriter log_writer )
 770             throws IOException {
 771         final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
 772         final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
 773         for( final String s : remapped ) {
 774             remapped_writer.println( s );
 775         }
 776         remapped_writer.close();
 777         System.out.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 778         log_writer.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 779     }
 780 }